A series of novel covalently linked waterborne polyurethane/3-aminopropyltriethoxysilane/multiwalled carbon nanotube (WPU/Si/MWCNT) nanocomposites were synthesized through an optimized copolycondensation of hydroxyls. A multiwalled carbon nanotube (MWCNT) as the inorganic filler was pretreated with a successive two-step modification route for its surface function with hydroxyl groups. 3-Aminopropyltriethoxysilane (APTES) was embedded into the backbone of the WPU molecules, hydrolysis of which generates silanol groups in the polyurethane (PU) matrix at the emulsification stage. Meanwhile, the silanol groups could condense with the hydroxyl groups on the surface of the modified MWCNT, generating the covalent bond between the modified MWCNT and the APTES-embedded PU matrix. The change of surface composition of the MWCNT during surface modification process was characterized by using both Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy. The transmission electron microscope (TEM) was utilized to image morphology of the modified MWCNT. The field emulsion scanning electron microscopy (SEM) micrographs and particle size distribution curves showed that the modified MWCNT was well dispersed in the PU matrix. The thermal stability, water resistance, mechanical properties and dynamic mechanical thermal behaviors of the WPU/Si/MWCNT films were characterized by thermogravimetric analysis, swelling test, tensile test, and dynamic mechanical thermal analysis, respectively. These results revealed that compared to the pristine WPU, the WPU/Si/MWCNT system with APTES and the modified MWCNT possesses outstanding water resistance, high thermal stability and excellent mechanical properties.